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84 results for “Medaka”
102 hpf medaka embryos in 96 well plate (4 embryo/well) - brightfield - 2X magnification - ACQUIFER Imaging Machine
<p>Dataset originates from:</p> <p>Gierten, J., Pylatiuk, C., Hammouda, O. T., Schock, C., Stegmaier, J., Wittbrodt, J., Gehrig, J. and Loosli, F. (2020). <strong>Automated high-throughput heartbeat quantification in medaka and zebrafish embryos under physiological conditions</strong>. Sci Rep <em>10</em>, 2046, doi:<a href="https://doi.org/10.1038/s41598-020-58563-w">10.1038/s41598-020-58563-w</a>.</p> <p>Used as benchmark dataset for Multi-Template-Matching by Thomas and Gehrig </p> <p>See implementation in Fiji <a href="https://github.com/LauLauThom/MultipleTemplateMatching">https://github.com/LauLauThom/MultipleTemplateMatching</a></p> <p>and in KNIME <a href="https://github.com/LauLauThom/MultipleTemplateMatching-KNIME">https://github.com/LauLauThom/MultipleTemplateMatching-KNIME</a></p> <p>Contacts: j.gehrig(at)acquifer.de, l.thomas(at)acquifer.de, jakob.gierten(at)cos.uni-heidelberg.de</p>
Hatchling Medaka Heart (HyLFM)
<p>dataset RDF to display https://www.ebi.ac.uk/biostudies/bioimages/studies/S-BSST604 on bioimage.io</p>
Evolution of size-fecundity relationship in medaka fish from different latitudes
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Dataset for: Passive dispersal potential of medaka's egg by attaching to waterbirds
<p>Original datasets of dehydration experiments used for our work "Freshwater fish egg dispersal by attaching to waterbirds", (under review).</p> <p>Analytic codes are deposited in GitHub(https://github.com/yaoakifumi/Medaka-embryo-desication-tolerance).</p> <p>The manuscript is also deposited in bioRxiv.</p> <p>doi: https://doi.org/10.1101/2024.03.11.584339</p>
Data and codes for "Habitat structural complexity increases age-class coexistence and population growth rate through relaxed cannibalism in medaka fish"
<p>The zip file contains readme files, as well as data and codes to reproduce results and figures from the paper.</p>
Population admixtures in medaka inferred by multiple arbitrary amplicon sequencing
<p>Cost-effective genotyping can be achieved by sequencing PCR amplicons. Short 3–10 base primers can arbitrarily amplify thousands of loci using only a few primers. To improve the sequencing efficiency of the multiple arbitrary amplicon sequencing (MAAS) approach, we designed new primers and examined their efficiency in sequencing and genotyping. To demonstrate the effectiveness of our method, we applied it to examine the population structure of the small freshwater fish, medaka (<em>Oryzias</em> <em>latipes</em>). We obtained 2,987 informative SNVs with no missing genotype calls for 67 individuals from 15 wild populations and three artificial strains. The estimated phylogenic and population genetic structures of the wild populations were consistent with previous studies, corroborating the accuracy of our genotyping method. We also attempted to reconstruct the genetic backgrounds of a commercial orange mutant strain, Himedaka, which has caused a genetic disturbance in wild populations. Our admixture analysis focusing on Himedaka showed that at least two wild populations had genetically contributed to the nuclear genome of this mutant strain. Our genotyping methods and results will be useful in quantitative assessments of genetic disturbance by this commercially available strain.</p>
Population admixtures in medaka inferred by multiple arbitrary amplicon sequencing
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Data from: Male medaka continue to mate with females despite sperm depletion
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Data from: A cryptic sex-linked locus revealed by the elimination of a master sex-determining locus in medaka fish
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Inter-population variation in fin sexual dimorphism in medaka (Oryzias latipes)
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Data from: Ontogenetic stage-specific quantitative trait loci contribute to divergence in developmental trajectories of sexually dimorphic fins between medaka populations
Sexual dimorphism can evolve when males and females differ in phenotypic optima. Genetic constraints can, however, limit the evolution of sexual dimorphism. One possible constraint is derived from alleles expressed in both sexes. Because males and females share most of their genome, shared alleles with different fitness effects between sexes are faced with intralocus sexual conflict. Another potential constraint is derived from genetic correlations between developmental stages. Sexually dimorphic traits are often favoured at adult stages, but selected against as juvenile, so developmental decoupling of traits between ontogenetic stages may be necessary for the evolution of sexual dimorphism in adults. Resolving intralocus conflicts between sexes and ages is therefore a key to the evolution of age-specific expression of sexual dimorphism. We investigated the genetic architecture of divergence in the ontogeny of sexual dimorphism between two populations of the Japanese medaka (Oryzias latipes) that differ in the magnitude of dimorphism in anal and dorsal fin length. Quantitative trait loci (QTL) mapping revealed that few QTL had consistent effects throughout ontogenetic stages and the majority of QTL change the sizes and directions of effects on fin growth rates during ontogeny. We also found that most QTL were sex-specific, suggesting that intralocus sexual conflict is almost resolved. Our results indicate that sex- and age-specific QTL enable the populations to achieve optimal developmental trajectories of sexually dimorphic traits in response to complex natural and sexual selection.
Scripts and metadata of the manuscript: Characterization of tmt-opsin2 in medaka fish provides insight into the interplay of light and temperature for behavioral regulation
<p>One of the big challenges in the study of animal behavior is to combine the molecular-level questions of functional genetics, typically performed in the lab, with meaningful combinations of environmental stimuli. Light and temperature are important external cues, influencing the behaviors of organisms. Thus, understanding the combined effect of light and temperature changes on wildtype versus genetically modified animals is a first step to understand the role of individual genes in the ability of animals to cope with changing environments.</p> <p>Many behavioral traits can be extrapolated from behavioral tests performed from automated motion tracking combined with machine learning. The acquired datasets, typically complex and large, can be challenging for subsequent quantitative analyses.</p> <p>Here we investigate medaka behavior of <em>tmt-opsin2</em> mutants versus corresponding wildtypes under different light and temperature conditions using automated tracking combined with a convolutional neuronal network and a Hidden Markov model-based approach. The temperatures in this study can occur in summer versus fall/winter in the natural habitat of medakafish. Under summer-like temperature, <em>tmt-opsin2</em> mutants did not exhibit changes in overall locomotion, consistent with previous observations. However, detailed analyses of fish position revealed that <em>tmt-opsin2 </em>mutants spent more time in central locations of the dish, possibly due to decreased anxiety. Furthermore, a clear difference in location and overall movement was obvious between mutant and wildtypes under colder conditions. These data indicate a role of <em>tmt-opsin2 </em>in behavioral adjustment, at least in part depending on the season.</p>
Diversity of sex chromosomes in Sulawesian medaka fishes
<p><span>Recent genetic and genomic studies have revealed tremendous diversity in sex chromosomes across diverse taxa. Closely related species with different sex chromosomes provide us with excellent opportunities to investigate the driving forces and the consequences of sex chromosome turnover. In the present study, we investigated the diversity of sex chromosomes of 13 <em>Oryzias</em> species from Sulawesi, Indonesia, which diversified during the last 4.86 million years. Using pooled sequencing we found sex chromosomes in 9 species that all had XY systems, with a species being possibly modified by multiple loci. Seven species (<em>O. woworae</em>, <em>O</em>. <em>asinua</em>, <em>O</em>. <em>wolasi</em>, <em>O</em>. <em>matanensis</em>, <em>O</em>. <em>celebensis</em>, <em>O</em>. <em>hadiatyae</em>, and <em>O</em>. <em>dopingdopingensis</em>) share linkage group (LG) 24 as sex chromosomes; however, they differed in the length and magnitude of sequence divergence between the X and Y chromosomes. The sex chromosome of <em>O</em>. <em>eversi</em> was LG4, which has not been reported as a sex chromosome in any other medaka species. In <em>O</em>. <em>sarasinorum</em>, LG16 and LG22 are associated with sex. Although LG16 was found to be sex-linked in another medaka species previously examined, the sex-determining regions did not overlap. No significant signatures for sex chromosomes were identified in the other 4 species (<em>O</em>. <em>marmoratus</em>, <em>O</em>. <em>nigrimas</em>, <em>O</em>. <em>nebulosus</em>, and <em>O</em>. <em>orthognathus</em>). Frequent turnovers and the great diversity of the sex chromosomes will make Sulawesian medaka species a model system for investigating the driving forces and consequences of sex chromosome turnover.</span></p>
Dataset Medaka fish mitochondrial oxygen fluxes
<p>Dataset of Medaka fish mitochondrial oxygen fluxes measured through a full factorial experimental design with (1) two ancestral temperatures: fish reared at 20 °C (C) or at 30 °C (W), and (2) two assay temperatures: mitochondrial oxygen fluxes measured at 20 °C or 30 °C.</p>
Data from: Genetic architecture of the variation in male-specific ossified processes on the anal fins of Japanese medaka
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Scripts and metadata of the manuscript: Characterization of tmt-opsin2 in medaka fish provides insight into the interplay of light and temperature for behavioral regulation
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Data from: Starvation causes female to male sex reversal through lipid metabolism in the teleost fish, medaka (Oryzias latipes)
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Data from: Ontogenetic stage-specific quantitative trait loci contribute to divergence in developmental trajectories of sexually dimorphic fins between medaka populations
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Diversity of sex chromosomes in Sulawesian medaka fishes
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Female preference for colour-enhanced males: a test of the sensory bias model in medaka, a drab fish
<p>Sexual selection research has long focused on the evolution of female mate preferences. Most of the models that have been developed posit that mate preferences evolve in a mating context. In contrast, the sensory bias model proposes that mate choice preferences arise in a non-mating context, as a by-product of natural selection acting on a female's perceptual system. Recent research has shown that many species of fishes, from across a large clade including poeciliids, goodeids, and medaka, have a bias for long wavelength (LW) colors (yellow, orange, red) in a non-mating context. Even species that do not have LW-colored ornaments, apparently because they have been lost secondarily, retain this latent bias for LW colors. Here, we predicted that female <i>Oryzias latipes </i>(Japanese medaka), a drab species with a latent preference for LW colors, would show a mate choice preference for males with an artificial secondary sexual trait—a colored stripe added to their flank. We confirmed that females were more responsive to red and orange objects in a non-mating context than to other colors. We also showed that females were less resistant towards males with a LW-colored stripe than to those enhanced with a non-LW stripe and that, for many females, responses towards specific LW colors were consistent across these non-mating and mating contexts. Therefore, our results provide support for the sensory bias model by providing a link between a sensory bias in a non-mating context and a mate choice preference in a drab species like medaka.</p>
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
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DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.